Journal articles 2012
Documents
Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association
Phumichai C, Chunwongse J, Jampatong S, Grudloyma P, Pulam T, Doungchan W, Wongkaew A and Kongsiri N (2012). Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association. Euphytica 187(3):369–379 (DOI: 10.1007/s10681-012-0699-8). Not open access; view abstract. (G4007.04)
Phumichai C, Chunwongse J, Jampatong S, Grudloyma P, Pulam T, Doungchan W, Wongkaew A and Kongsiri N (2012). Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association. Euphytica 187(3):369–379 (DOI: 10.1007/s10681-012-0699-8). Not open access; view abstract. (G4007.04)
Matita, a new retroelement from peanut: Characterization and evolutionary context in the light of the Arachis A–B genome divergence
Nielen S, Vidigal BS, Leal-Bertioli SCM, Ratnaparkhe M, Paterson AH, Garsmeur O, D'Hont A, Guimarães PM and Bertioli D (2012). Matita, a new retroelement from peanut: Characterization and evolutionary context in the light of the Arachis A–B genome divergence. Molecular Genetics and Genomics 287(1):21–38 (DOI: 10.1007/s00438-011-0656-6). First published online in November 2011. Not open access; view abstract. (G6010.01)
Nielen S, Vidigal BS, Leal-Bertioli SCM, Ratnaparkhe M, Paterson AH, Garsmeur O, D'Hont A, Guimarães PM and Bertioli D (2012). Matita, a new retroelement from peanut: Characterization and evolutionary context in the light of the Arachis A–B genome divergence. Molecular Genetics and Genomics 287(1):21–38 (DOI: 10.1007/s00438-011-0656-6). First published online in November 2011. Not open access; view abstract. (G6010.01)
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
Guimarães PM, Brasileiro ACM, Morgante CV, Martins ACQ, Pappas G, Silva OB, Togawa R, Leal-Bertioli SCM, Araujo ACG, Moretzsohn MC and Bertioli DJ (2012). Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics 13:387 (DOI: 10.1186/1471-2164-13-387). (G6010.01)
Abstract: Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.
Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.
Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
Guimarães PM, Brasileiro ACM, Morgante CV, Martins ACQ, Pappas G, Silva OB, Togawa R, Leal-Bertioli SCM, Araujo ACG, Moretzsohn MC and Bertioli DJ (2012). Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics 13:387 (DOI: 10.1186/1471-2164-13-387). (G6010.01)
Abstract: Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.
Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.
Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
Full article
TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici in wheat
Tufan HA, McGrann GRD, MacCormack R and Boyd LA (2012). TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici in wheat. Molecular Plant Pathology 13(7):653–665 (DOI: 10.1111/j.1364-3703.2011.00775.x). Not open access; view abstract. (G3005.11)
Tufan HA, McGrann GRD, MacCormack R and Boyd LA (2012). TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici in wheat. Molecular Plant Pathology 13(7):653–665 (DOI: 10.1111/j.1364-3703.2011.00775.x). Not open access; view abstract. (G3005.11)
Field evaluation on functional roles of root plastic responses on dry matter production and grain yield of rice under cycles of transient soil moisture stresses using chromosome segment substitution lines
Niones JM, Suralta RR, Inukai Y and Yamauchi A (2012). Field evaluation on functional roles of root plastic responses on dry matter production and grain yield of rice under cycles of transient soil moisture stresses using chromosome segment substitution lines. Plant and Soil 359(1-2):107–120. (DOI: 10.1007/s11104-012-1178-7). (G3008.06). Not open access: view abstract
Niones JM, Suralta RR, Inukai Y and Yamauchi A (2012). Field evaluation on functional roles of root plastic responses on dry matter production and grain yield of rice under cycles of transient soil moisture stresses using chromosome segment substitution lines. Plant and Soil 359(1-2):107–120. (DOI: 10.1007/s11104-012-1178-7). (G3008.06). Not open access: view abstract
Genetic diversity in Iranian chickpea (Cicer arietinum L.) landraces as revealed by microsatellite markers
Naghavi MR, Monfared SR and Gomez H (2012). Genetic diversity in Iranian chickpea (Cicer arietinum L.) landraces as revealed by microsatellite markers. Czech Journal of Genetics and Plant Breeding 48(3):131–138.
Abstract: To estimate the genetic diversity of chickpea germplasm from Iran, a total of 307 landraces from 4 regions including: northern areas (29 from Ardebil, 3 from Qazvin and 5 from Mazanderan provinces), temperate (16 from Kermanshah, 2 from Semnan, 54 from Khorasan and 20 from Kerman provinces), semi-arid (28 from Ghom and 56 from Isfahan provinces) and cold areas (15 from West Azarbayjan, 52 from Tehran and 27 from East Azarbayjan provinces) were analysed using 16 microsatellite loci. The number of alleles per microsatellite locus ranged from 8 to 29, with an average of 19.31 per locus. A high level of genetic diversity in the northern area (He = 0.76), even with a limited number of available landraces (37) compared with the other three regions (84–94), might confirm the northern Persia as part of the chickpea centre of origin. The neighbour-joining tree showed a low relationship between molecular divergence and the geographical grouping of chickpea. Moreover, cluster analyses based on molecular data showed that the northern area was separated clearly from the other three regions, indicating a physical barrier or geographical and environmental differences among these regions. A wide genetic diversity of Iranian chickpea landraces is a critical component for future selection and use of this germplasm for future breeding of chickpea.
Naghavi MR, Monfared SR and Gomez H (2012). Genetic diversity in Iranian chickpea (Cicer arietinum L.) landraces as revealed by microsatellite markers. Czech Journal of Genetics and Plant Breeding 48(3):131–138.
Abstract: To estimate the genetic diversity of chickpea germplasm from Iran, a total of 307 landraces from 4 regions including: northern areas (29 from Ardebil, 3 from Qazvin and 5 from Mazanderan provinces), temperate (16 from Kermanshah, 2 from Semnan, 54 from Khorasan and 20 from Kerman provinces), semi-arid (28 from Ghom and 56 from Isfahan provinces) and cold areas (15 from West Azarbayjan, 52 from Tehran and 27 from East Azarbayjan provinces) were analysed using 16 microsatellite loci. The number of alleles per microsatellite locus ranged from 8 to 29, with an average of 19.31 per locus. A high level of genetic diversity in the northern area (He = 0.76), even with a limited number of available landraces (37) compared with the other three regions (84–94), might confirm the northern Persia as part of the chickpea centre of origin. The neighbour-joining tree showed a low relationship between molecular divergence and the geographical grouping of chickpea. Moreover, cluster analyses based on molecular data showed that the northern area was separated clearly from the other three regions, indicating a physical barrier or geographical and environmental differences among these regions. A wide genetic diversity of Iranian chickpea landraces is a critical component for future selection and use of this germplasm for future breeding of chickpea.
A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae)
Billot C, Rivallan R, Sall MN, Fonceka D, Deu M, Glaszmann J-C, Noyer J-L, Rami J-F, Risterucci A-M, Wincker P, Ramu P and Hash CT (2012). A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae). American Journal of Botany 99(6):e245–e250. (DOI: 10.3732/ajb.1100548).
Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers.
Billot C, Rivallan R, Sall MN, Fonceka D, Deu M, Glaszmann J-C, Noyer J-L, Rami J-F, Risterucci A-M, Wincker P, Ramu P and Hash CT (2012). A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae). American Journal of Botany 99(6):e245–e250. (DOI: 10.3732/ajb.1100548).
Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers.
Probability of success of breeding strategies for improving pro-vitamin A content in maize
Zhang X, Pfeiffer WH, Palacios-Rojas N, Babu R, Bouis H and Wang J (20102). Probability of success of breeding strategies for improving pro-vitamin A content in maize. Theoretical and Applied Genetics 125(2):235–246. (DOI: 10.1007/s00122-012-1828-4). (IBP project, G8009) Not open access: view abstract
Zhang X, Pfeiffer WH, Palacios-Rojas N, Babu R, Bouis H and Wang J (20102). Probability of success of breeding strategies for improving pro-vitamin A content in maize. Theoretical and Applied Genetics 125(2):235–246. (DOI: 10.1007/s00122-012-1828-4). (IBP project, G8009) Not open access: view abstract
QTL Analysis for root protein in a backcross family of cassava derived from Manihot esculenta ssp flabellifolia
Akinbo O, Labuschagne MT, Marín J, Ospina C, Santos L, Barrera E, Gutiérrez J, Ewa F, Okogbenin E, Fregene M (2012). QTL Analysis for root protein in a backcross family of cassava derived from Manihot esculenta ssp flabellifolia. Tropical Plant Biology Published online 21 February 2012. 12pp. (DOI: 10.1007/s12042-012-9095-8). Not open access: view abstract
Akinbo O, Labuschagne MT, Marín J, Ospina C, Santos L, Barrera E, Gutiérrez J, Ewa F, Okogbenin E, Fregene M (2012). QTL Analysis for root protein in a backcross family of cassava derived from Manihot esculenta ssp flabellifolia. Tropical Plant Biology Published online 21 February 2012. 12pp. (DOI: 10.1007/s12042-012-9095-8). Not open access: view abstract
Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding
Foncéka D, Tossim HA, Rivallan R, Vignes H, Faye I, Ndoye O, Moretzsohn MC, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF (2012). Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biology 2012, 12:26 45pp. (DOI: 10.1186/1471-2229-12-26, ISSN 1471-2229).
Foncéka D, Tossim HA, Rivallan R, Vignes H, Faye I, Ndoye O, Moretzsohn MC, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF (2012). Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biology 2012, 12:26 45pp. (DOI: 10.1186/1471-2229-12-26, ISSN 1471-2229).
